A Monte Carlo Simulation Study of Ion Distribution and Osmotic Pressure
in Hexagonally Oriented DNA.
J.Phys.Chem. v.99, p.10373-82 (1995)
Alexander P. Lyubartsev and
Lars Nordenskiold
(Division of Physical Chemistry, Arrhenius laboratory, Stockholm University,
S-106 91, Stockholm, SWEDEN)
Abstract.
The electrostatic osmotic pressure in a system of hexagonally
packed DNA molecules has been calculated with the Monte Carlo (MC)
simulation method. The DNA molecules were modeled as hard cylinders with
charged groups located at the sites corresponding to B-DNA, with the ions
considered as point charges with repulsive r-12 potentials, and the solvent
treated as a dielectric medium. Periodic boundary conditions for a hexagonal
cell were used with Ewald summation of the electrostatic interactions.
The pressure was calculated from the relation P=-DF/DV, where differences
of free energies F, were obtained with the expanded ensemble method. The
calculations were carried out both for salt free solutions and for solutions
containing added salt; in the latter case the simulations were performed
within the grand canonical ensemble. In the system with only monovalent
ions, the forces between DNA were found to be always repulsive. In the case
of divalent counterions, an effective attraction between DNA molecules may
appear for distances of 5-15 between the surfaces, depending on the ion
size and salt concentration. The results of the simulations showed that a
correct statistical-mechanical treatment of the electrostatic interactions
in the frame of a continuum dielectric model, can reproduce the essential
features of available experimental data, indicating that this contribution
to the pressure is an important contributor to the experimentally observed
presurre versus distance curves for ordered DNA.